Scientists use genome sequencing to halt superbug outbreak

LONDON (Reuters) - Researchers have used DNA sequencing for the first time to identify, analyze and put a halt to an infectious disease outbreak in a hospital.

The success of the technique, which used fast genome sequencing technology to control an outbreak of the MRSA superbug on a baby ward, suggests it could be used to control hospital bugs, salmonella and E.coli infections and diseases like tuberculosis, scientists said.

"What we have glimpsed through this pioneering study is a future in which new sequencing methods will help us to identify, manage and stop hospital outbreaks," said Nick Brown, an infection control doctor at Addenbrooke's Hospital Cambridge, who co-led the study and presented the findings at a briefing.

MRSA, or methicillin-resistant staphylococcus aureus, is a drug-resistant bacterial infection, or superbug, and a serious public health problem. When outbreaks occur in hospitals it can lead to the closure of whole wards with many people infected.

The bug kills an estimated 19,000 people in the United States per year. Although rates of MRSA infection have come down significantly in Britain in recent years, it still presents a major threat with several hundred deaths a year and high hospital costs involved in managing infected patients.

Julian Parkhill from Britain's Sanger Institute, who also worked on the study, said there is a "real health and cost burden from hospital outbreaks" which could be significantly reduced or eliminated if they were contained swiftly.

In the study, staff at Addenbrooke's hospital using routine screening over a six month period found 12 patients carrying MRSA. Because they were only using standard tests, which provide limited information, the infection control team was not able to tell if the 12 were part of an outbreak, or were unconnected cases that did not present a threat.

MRSA is a bug present in around one percent of the population at any time, and does not always cause infection.

Parkhill and Brown's team analyzed MRSA samples from the 12 patients with DNA sequencing technology and found that all the MRSA bacteria were closely related, confirming an outbreak.

By tracing relatives and other people who had recent links to the hospital, they also found the outbreak was more extensive than previously thought, with twice as many people carrying or infected with the MRSA strain.

While this sequencing study was underway, the hospital's infection control team found a MRSA case in the special care baby unit - 64 days after the last MRSA patient had left.

The team used advanced DNA sequencing to show in real time that this strain was also part of the same outbreak, raising the possibility that a staff member was unknowingly carrying and transmitting the MRSA strain.

After screening 154 staff they found one carrying MRSA and, using DNA sequencing, confirmed it was the strain linked to the outbreak. The worker was quickly treated to eradicate the bug, and any further spread was stopped.

The researchers, whose findings were published in the Lancet Infectious Diseases journal, say this kind of fast genome sequencing could eventually form the basis for regional or national infection surveillance program designed to nip infectious disease outbreaks in the bud.

"This technology holds great promise for the quick and accurate identification of bacterial transmissions in our hospitals and could lead to a paradigm shift in how we manage infection control and practice," said Parkhill.

It could also be used for outbreaks of food-borne infections like salmonella or E.coli. Genome sequencing was used in an E.coli outbreak in Europe in 2011, but only in the latter stages to help identify the source.